The specific functions of lipids are related to their chemical and physical properties and depend on specific molecular structures. Despite technological advancements that have made mass spectrometry (MS) an essential tool for biomolecule analysis, unequivocal assignment of lipid positional and stereo isomers remains a fundamentally challenging task. The primary goal of this project is to develop a MS- based instrument platform that is capable of elucidating lipid structures in complex lipidomic samples in a high throughput manner and with significantly improved sensitivity and specificity. This analytical platform will be primarily based on a triple quadrupole mass spectrometer modified to have the capability of high efficiency ozone induced dissociation (OzID) for lipids double bond positional isomer identification. Its sensitivity, dynamic range and measurement specificity will be significantly enhanced by integrating with electrodynamic ion funnel-based MS interface technology and high resolution field asymmetric waveform ion mobility spectrometry (FAIMS) technology. The applications of this FAIMS/OzID MS instrument platform will be demonstrated by analyzing human plasma samples of a type 2 diabetes cohort to achieve unambiguous and complete structural elucidation of lipid biomarkers. The resulting instrument platform is expected to have broad applications in structural identification of intact lipids and will aid discovery and verification of lipid biomarkers in biomedical applications in addition to providing insights into functional roles of diverse lipid species.